prysm.detector¶
Detectorrelated simulations.

class
prysm.detector.
Detector
(pitch_x=None, pitch_y=None, pixel='rectangle', resolution=(1024, 1024), nbits=16, framebuffer=10)¶ Bases:
object
Model of a image sensor.

capture
(convolvable)¶ Sample a convolvable, mimics capturing a photo of an oversampled representation of an image.
 Parameters
convolvable (prysm.Convolvable) – a convolvable object
 Returns
a new convolvable object, as it would be sampled by the detector
 Return type
prysm.convolvable
 Raises
ValueError – if the convolvable would have to become supersampled by the detector; this would lead to an inaccurate result and is not supported

save_image
(path, which='last')¶ Save an image captured by the detector.
 Parameters
path (string) – path to save the image to
which (string or int) – if string, “first” or “last”, otherwise index into the capture buffer of the camera.
 Raises
ValueError – bad target frame to save; should always be the a valid int < buffer_depth

show_image
(which='last', fig=None, ax=None)¶ Show an image captured by the detector.
 Parameters
which (string or int) – if string, “first” or “last”, otherwise index into the capture buffer of the camera
fig (matplotlib.figure.Figure, optional) – Figure containing the plot
ax (matplotlib.axes.Axis, optional) – Axis containing the plot
 Returns
fig (`matplotlib.figure.Figure) – Figure containing the plot
ax (matplotlib.axes.Axis) – Axis containing the plot

pitch
¶ 1D pixel pitch  minimum of x/y pitches.

fill_factor_x
¶ Fill factor in the X axis.

fill_factor_y
¶ Fill factor in the Y axis.

fill_factor
¶ 1D fill factor – minimum of x/y fill factors.

fs
¶ Sampling frequency in cy/mm.

nyquist
¶ Nyquist frequency in cy/mm.

last
¶ Last frame captured.


class
prysm.detector.
OLPF
(width_x, width_y=None, sample_spacing=0, samples_x=None, samples_y=None)¶ Bases:
prysm.convolution.Convolvable
Optical Low Pass Filter.

analytic_ft
(x, y)¶ Analytic fourier transform of a pixel aperture.
 Parameters
x (numpy.ndarray) – sample points in x axis
y (numpy.ndarray) – sample points in y axis
 Returns
2D numpy array containing the analytic fourier transform
 Return type
numpy.ndarray

center_x
¶ Center “pixel” in x.

center_y
¶ Center “pixel” in y.

conv
(other)¶ Convolves this convolvable with another.
 Parameters
other (Convolvable) – A convolvable object
 Returns
a convolvable object
 Return type
Convolvable
Notes
If self and other both have analytic Fourier transforms, no math will be done and the aFTs are merged directly.
If only one of self or other has an analytic Fourier transform, the output grid will be defined by the object which does not have an analytic Fourier transform.
If neither has an analytic transform, the output grid will:  span max(self.support, other.support)  have sample spacing min(self.sample_spacing, other.sample_spacing)
This ensures the signal remains Nyquist sampled and (probably) doesn’t expand beyond the extent of the output window. The latter condition will be violated when two large convolvables are convolved.

copy
()¶ Return a (deep) copy of this instance.

deconv
(other, balance=1000, reg=None, is_real=True, clip=False, postnormalize=True)¶ Perform the deconvolution of this convolvable object by another.
 Parameters
other (Convolvable) – another convolvable object, used as the PSF in a Wiener deconvolution
balance (float, optional) – regularization parameter; passed through to skimage
reg (numpy.ndarray, optional) – regularization operator, passed through to skimage
is_real (bool, optional) – True if self and other are both real
clip (bool, optional) – clips self and other into (0,1)
postnormalize (bool, optional) – normalize the result such that it falls in [0,1]
 Returns
a new Convolable object
 Return type
Convolvable
Notes
See skimage: http://scikitimage.org/docs/dev/api/skimage.restoration.html#skimage.restoration.wiener

static
from_file
(path, scale)¶ Read a monochrome 8 bit per pixel file into a new Image instance.
 Parameters
path (string) – path to a file
scale (float) – pixel scale, in microns
 Returns
a new image object
 Return type
Convolvable

plot_slice_xy
(axlim=20, lw=3, zorder=3, fig=None, ax=None)¶ Create a plot of slices through the X and Y axes of the PSF.
 Parameters
axlim (float or int, optional) – axis limits, in microns
lw (float, optional) – line width
zorder (int, optional) – zorder
fig (matplotlib.figure.Figure, optional) – Figure to draw plot in
ax (matplotlib.axes.Axis) – Axis to draw plot in
 Returns
fig (matplotlib.figure.Figure, optional) – Figure containing the plot
ax (matplotlib.axes.Axis, optional) – Axis containing the plot

renorm
()¶ Renormalize so that the peak is at a value of unity.

sample_spacing
¶ centertocenter sample spacing.

samples_x
¶ Number of samples in the x dimension.

samples_y
¶ Number of samples in the y dimension.

save
(path, nbits=8)¶ Write the image to a png, jpg, tiff, etc.
 Parameters
path (string) – path to write the image to
nbits (int) – number of bits in the output image

shape
¶ Proxy to phase or data shape.

show
(xlim=None, ylim=None, interp_method=None, power=1, show_colorbar=True, fig=None, ax=None)¶ Display the image.
 Parameters
xlim (iterable, optional) – x axis limits
ylim (iterable,) – y axis limits
interp_method (string) – interpolation technique used in display
power (float) – inverse of power to stretch image by. E.g. power=2 will plot img ** (1/2)
show_colorbar (bool) – whether to show the colorbar or not.
fig (matplotlib.figure.Figure, optional:) – Figure containing the plot
ax (matplotlib.axes.Axis, optional:) – Axis containing the plot
 Returns
fig (matplotlib.figure.Figure, optional:) – Figure containing the plot
ax (matplotlib.axes.Axis, optional:) – Axis containing the plot

show_fourier
(freq_x=None, freq_y=None, interp_method='lanczos', fig=None, ax=None)¶ Display the fourier transform of the image.
 Parameters
interp_method (string) – method used to interpolate the data for display.
freq_x (iterable) – x frequencies to use for convolvable with analytical FT and no data
freq_y (iterable) – y frequencies to use for convolvable with analytic FT and no data
fig (matplotlib.figure.Figure) – Figure containing the plot
ax (matplotlib.axes.Axis) – Axis containing the plot
 Returns
fig (matplotlib.figure.Figure) – Figure containing the plot
ax (matplotlib.axes.Axis) – Axis containing the plot
Notes
freq_x and freq_y are unused when the convolvable has a .data field.

size
¶ Proxy to phase or data size.

slice_x
¶ Retrieve a slice through the X axis of the phase.
 Returns
self.unit (numpy.ndarray) – ordinate axis
slice of self.phase or self.data (numpy.ndarray)

slice_y
¶ Retrieve a slice through the Y axis of the phase.
 Returns
self.unit (numpy.ndarray) – ordinate axis
slice of self.phase or self.data (numpy.ndarray)

support
¶ Width of the domain.

support_x
¶ Width of the domain in X.

support_y
¶ Width of the domain in Y.


class
prysm.detector.
PixelAperture
(width_x, width_y=None, sample_spacing=0, samples_x=None, samples_y=None)¶ Bases:
prysm.convolution.Convolvable
The aperture of a rectangular pixel.

analytic_ft
(x, y)¶ Analytic fourier transform of a pixel aperture.
 Parameters
x (numpy.ndarray) – sample points in x axis
y (numpy.ndarray) – sample points in y axis
 Returns
2D numpy array containing the analytic fourier transform
 Return type
numpy.ndarray

center_x
¶ Center “pixel” in x.

center_y
¶ Center “pixel” in y.

conv
(other)¶ Convolves this convolvable with another.
 Parameters
other (Convolvable) – A convolvable object
 Returns
a convolvable object
 Return type
Convolvable
Notes
If self and other both have analytic Fourier transforms, no math will be done and the aFTs are merged directly.
If only one of self or other has an analytic Fourier transform, the output grid will be defined by the object which does not have an analytic Fourier transform.
If neither has an analytic transform, the output grid will:  span max(self.support, other.support)  have sample spacing min(self.sample_spacing, other.sample_spacing)
This ensures the signal remains Nyquist sampled and (probably) doesn’t expand beyond the extent of the output window. The latter condition will be violated when two large convolvables are convolved.

copy
()¶ Return a (deep) copy of this instance.

deconv
(other, balance=1000, reg=None, is_real=True, clip=False, postnormalize=True)¶ Perform the deconvolution of this convolvable object by another.
 Parameters
other (Convolvable) – another convolvable object, used as the PSF in a Wiener deconvolution
balance (float, optional) – regularization parameter; passed through to skimage
reg (numpy.ndarray, optional) – regularization operator, passed through to skimage
is_real (bool, optional) – True if self and other are both real
clip (bool, optional) – clips self and other into (0,1)
postnormalize (bool, optional) – normalize the result such that it falls in [0,1]
 Returns
a new Convolable object
 Return type
Convolvable
Notes
See skimage: http://scikitimage.org/docs/dev/api/skimage.restoration.html#skimage.restoration.wiener

static
from_file
(path, scale)¶ Read a monochrome 8 bit per pixel file into a new Image instance.
 Parameters
path (string) – path to a file
scale (float) – pixel scale, in microns
 Returns
a new image object
 Return type
Convolvable

plot_slice_xy
(axlim=20, lw=3, zorder=3, fig=None, ax=None)¶ Create a plot of slices through the X and Y axes of the PSF.
 Parameters
axlim (float or int, optional) – axis limits, in microns
lw (float, optional) – line width
zorder (int, optional) – zorder
fig (matplotlib.figure.Figure, optional) – Figure to draw plot in
ax (matplotlib.axes.Axis) – Axis to draw plot in
 Returns
fig (matplotlib.figure.Figure, optional) – Figure containing the plot
ax (matplotlib.axes.Axis, optional) – Axis containing the plot

renorm
()¶ Renormalize so that the peak is at a value of unity.

sample_spacing
¶ centertocenter sample spacing.

samples_x
¶ Number of samples in the x dimension.

samples_y
¶ Number of samples in the y dimension.

save
(path, nbits=8)¶ Write the image to a png, jpg, tiff, etc.
 Parameters
path (string) – path to write the image to
nbits (int) – number of bits in the output image

shape
¶ Proxy to phase or data shape.

show
(xlim=None, ylim=None, interp_method=None, power=1, show_colorbar=True, fig=None, ax=None)¶ Display the image.
 Parameters
xlim (iterable, optional) – x axis limits
ylim (iterable,) – y axis limits
interp_method (string) – interpolation technique used in display
power (float) – inverse of power to stretch image by. E.g. power=2 will plot img ** (1/2)
show_colorbar (bool) – whether to show the colorbar or not.
fig (matplotlib.figure.Figure, optional:) – Figure containing the plot
ax (matplotlib.axes.Axis, optional:) – Axis containing the plot
 Returns
fig (matplotlib.figure.Figure, optional:) – Figure containing the plot
ax (matplotlib.axes.Axis, optional:) – Axis containing the plot

show_fourier
(freq_x=None, freq_y=None, interp_method='lanczos', fig=None, ax=None)¶ Display the fourier transform of the image.
 Parameters
interp_method (string) – method used to interpolate the data for display.
freq_x (iterable) – x frequencies to use for convolvable with analytical FT and no data
freq_y (iterable) – y frequencies to use for convolvable with analytic FT and no data
fig (matplotlib.figure.Figure) – Figure containing the plot
ax (matplotlib.axes.Axis) – Axis containing the plot
 Returns
fig (matplotlib.figure.Figure) – Figure containing the plot
ax (matplotlib.axes.Axis) – Axis containing the plot
Notes
freq_x and freq_y are unused when the convolvable has a .data field.

size
¶ Proxy to phase or data size.

slice_x
¶ Retrieve a slice through the X axis of the phase.
 Returns
self.unit (numpy.ndarray) – ordinate axis
slice of self.phase or self.data (numpy.ndarray)

slice_y
¶ Retrieve a slice through the Y axis of the phase.
 Returns
self.unit (numpy.ndarray) – ordinate axis
slice of self.phase or self.data (numpy.ndarray)

support
¶ Width of the domain.

support_x
¶ Width of the domain in X.

support_y
¶ Width of the domain in Y.


prysm.detector.
pixelaperture_analytic_otf
(width_x, width_y, freq_x, freq_y)¶ Analytic MTF of a rectangular pixel aperture.
 Parameters
width_x (float) – x diameter of the pixel, in microns
width_y (float) – y diameter of the pixel, in microns
freq_x (numpy.ndarray) – x spatial frequency, in cycles per micron
freq_y (numpy.ndarray) – y spatial frequency, in cycles per micron
 Returns
MTF of the pixel aperture
 Return type
numpy.ndarray

prysm.detector.
bindown
(array, nsamples_x, nsamples_y=None, mode='avg')¶ Bin (resample) an array.
 Parameters
array (numpy.ndarray) – array of values
nsamples_x (int) – number of samples in x axis to bin by
nsamples_y (int) – number of samples in y axis to bin by. If None, duplicates value from nsamples_x
mode (str, {‘avg’, ‘sum’}) – sum or avg, how to adjust the output signal
 Returns
ndarray binned by given number of samples
 Return type
numpy.ndarray
Notes
Array should be 2D. TODO: patch to allow 3D data.
If the size of array is not evenly divisible by the number of samples, the algorithm will trim around the border of the array. If the trim length is odd, one extra sample will be lost on the left side as opposed to the right side.
 Raises
ValueError – invalid mode

prysm.detector.
bindown_with_units
(px_x, px_y, source_spacing, source_data)¶ Perform bindown, returning unit axes and data.
 Parameters
px_x (float) – pixel pitch in the x direction, microns
px_y (float) – pixel pitch in the y direction, microns
source_spacing (float) – pixel pitch in the source data, microns
source_data (numpy.ndarray) – ndarray of regularly spaced data
 Returns
ux (numpy.ndarray) – 1D array of sample coordinates in the x direction
uy (numpy.ndarray) – 1D array of sample coordinates in the y direction
data (numpy.ndarray) – binneddown data